PDBinfGet: Get all available PDB_ID information of the genelist you...

In windforclouds/PSV2N: This is a shortest path-based algorithm named PS-V2N.

Description

we acquire information of PDB_ID in virtue of the api of EMBL protein(https://www.ebi.ac.uk/proteins/api/proteins/),you just need to input a vector of genelist in your hand.

Usage

PDBinfGet(genelist,
          show.length = FALSE,
          id.fromType = "hgnc_symbol",
          id.biomart  = ENSEMBL_MART_ENSEMBL,
          id.dataset  = "hsapiens_gene_ensembl",
          id.toType   = "uniprot_gn_id"

Arguments

genelist	a vector of gene(s)
show.length	determines whether the length is displayed,default FALSE
id.fromType	input id type(must be same as type of input genelist), we set 4 frequently-used types here, which are "hgnc_symbol","entrezgene_id","ensembl_gene_id","uniprot_gn_id"
id.biomart	biomart types when id needs to be translated, see also getBM
id.dataset	biomart dataset choose, see also getBM
id.toType	output id type

Value

properties of PDB_ID,such as method of Protein crystal analysis, resolution,chains,structure length

Author(s)

Ji Yang

Examples

#input type is "hgnc_symbol":
PDBinfGet(genelist    = vertex_sample[1:5,1],
          show.length = FALSE,
          id.fromType = "hgnc_symbol",
          id.biomart  = ENSEMBL_MART_ENSEMBL,
          id.dataset  = "hsapiens_gene_ensembl",
          id.toType   = "uniprot_gn_id")
#input type is "uniprot_gn_id":
PDBinfGet(genelist    = "P21580",
          show.length = FALSE,
          id.fromType = "uniprot_gn_id",
          id.biomart  = ENSEMBL_MART_ENSEMBL,
          id.dataset  = "hsapiens_gene_ensembl",
          id.toType   = "uniprot_gn_id")

windforclouds/PSV2N documentation built on Dec. 23, 2021, 5:15 p.m.